Rare Molecular Variants of Gastrointestinal Stromal Tumors (GISTs): Clinical Implications and Overview of Current Evidence

Abstract

Gastrointestinal stromal tumors are the most common sarcomas of the gastrointestinal tract. They are characterized by a distinct molecular profile, most frequently involving activating mutations in the KIT or PDGFRA genes, the identification of which has enabled the development of effective targeted therapies and has significantly improved patient outcomes. Despite significant therapeutic advances, treatment with tyrosine kinase inhibitors remains associated with the risk of primary or secondary resistance in a subset of patients. This phenomenon has highlighted the considerable biological heterogeneity of gastrointestinal stromal tumor, encompassing not only canonical mutational variants but also rare molecular alterations with distinct pathogenic mechanisms and clinical implications. Growing evidence suggests that detailed molecular characterization of gastrointestinal stromal tumors is of critical clinical importance, enabling improved risk stratification, optimization of treatment selection, and identification of patients requiring alternative therapeutic strategies. Therefore, comprehensive molecular diagnostics should be an integral part of the diagnostic and therapeutic approach to this heterogeneous group of tumors. The aim of this study is to provide an overview of current knowledge on rare molecular variants of gastrointestinal stromal tumors, as well as the available data on their clinical course and sensitivity to tyrosine kinase inhibitors and other therapeutic strategies.

Key Points

Rare molecular variants constitute an important but often under-recognized subgroup of gastrointestinal stromal tumors, with distinct biological and clinical characteristics that influence treatment sensitivity, resistance mechanisms, and clinical outcomes while underscoring the growing importance of comprehensive molecular diagnostics in routine clinical practice.

Comprehensive molecular diagnostics, including next-generation sequencing, enables accurate classification of rare gastrointestinal stromal tumor subtypes, improves risk stratification, and supports selection of the most appropriate targeted therapy, particularly in tumors lacking canonical KIT or platelet-derived growth factor receptor alpha mutations.

This review summarizes current evidence on rare molecular variants of gastrointestinal stromal tumors, highlights their biological and clinical significance, and provides a practical overview of contemporary molecular diagnostic strategies for identifying clinically actionable alterations.

Introduction

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract, originating from interstitial Cajal cells or precursor cells with similar characteristics [1]. The disease most often affects the stomach and small intestine and is primarily diagnosed in older adults (in their 50s), although it can occur in any part of the gastrointestinal tract and also in younger patients, including those with genetic predisposition syndromes [1, 2]. Although GISTs are rare in the general population (about 10–15 new cases per million people annually), they are a model example of a neoplasm in which the identification of key molecular abnormalities has directly led to the development of effective targeted therapies [2].

From a biological and genetic perspective, GISTs constitute a unique group of sarcomas, defined primarily by the presence of activating mutations in genes encoding tyrosine kinase receptors, mainly KIT and PDGFRA [3]. The discovery of these abnormalities marked the beginning of the era of targeted GIST treatment and radically improved prognosis. Before the introduction of tyrosine kinase inhibitors, treatment was limited almost exclusively to surgical resection, and the high recurrence rate, combined with the lack of effective systemic therapy options for advanced disease, resulted in low long-term survival rates. The use of imatinib, both as adjuvant therapy and for metastatic disease, followed by subsequent lines of treatment (sunitinib, regorafenib, ripretinib), has significantly prolonged survival and enabled durable control of the disease in a substantial proportion of patients [4–6].

At the same time, it is becoming increasingly clear in clinical practice that GISTs are not a homogeneous disease entity, and that the effectiveness of treatment with tyrosine kinase inhibitors depends largely on the molecular profile of the tumor. In addition to the most common mutations in exons 11 and 9 of the KIT gene and mutations in the PDGFRA gene (in 80% of patients), the molecular spectrum of GISTs includes rare mutation variants within classical driver genes as well as a heterogeneous group of tumors lacking KIT/PDGFRA mutations, referred to as wild-type GISTs (about 10–15%). These abnormalities are associated with different biological characteristics and clinical courses of the disease as well as significant differences in sensitivity and mechanisms of resistance to targeted therapy.

Despite remarkable therapeutic advances, resistance to tyrosine kinase inhibitors remains a key clinical challenge in the treatment of GISTs, particularly in patient subgroups with rare molecular abnormalities. In these cases, standard treatment regimens are often limited in their efficacy, and clinical decisions require in-depth molecular analysis and an individualized approach. As genetic diagnostic methods advance, the importance of precise molecular classification of GISTs is growing, making it a key component of modern personalized treatment. The aim of this study is to review current data on rare molecular variants of GIST and their clinical significance, with particular emphasis on the impact of the tumor genetic profile on the effectiveness of treatment with tyrosine kinase inhibitors, mechanisms of resistance, and potential directions for further development of targeted therapies.

Typical Clinical, Immunohistochemical, and Molecular Features of Gastrointestinal Stromal Tumors (GISTs)

Gastrointestinal stromal tumors are typically well-defined mesenchymal neoplasms that develop from the muscular layer of the gastrointestinal tract wall. The most common location of GIST is the stomach (about 60% of cases), as well as the small intestine, mainly the jejunum and ileum (about 30%). These tumors rarely occur in the duodenum (4–5%), rectum (about 4%), colon and appendix (1–2%), and esophagus (< 1%) [7]. Extraintestinal GISTs, found in the mesentery, omentum, or retroperitoneal space, may represent metastases from an undiagnosed primary site in the gastrointestinal tract or, less commonly, a distinct entity with morphology and a molecular profile consistent with GIST [7, 8].

Sporadic GISTs are most often diagnosed in adults, primarily in their 50s, with a slight predominance of cases in men [9]. Tumors occurring in children and adolescents account for a small but clinically significant proportion of cases and are usually characterized by a different tumor biology. This group is dominated by wild-type GISTs, which are often associated with succinate dehydrogenase (SDH) deficiency and exhibit specific clinical, pathomorphological, and molecular characteristics [10].

Histologically, GISTs show varied morphology and may present as spindle-cell (about 70% of cases), epithelioid-cell (about 20%), or mixed-type tumors (about 10%) [11]. Immunohistochemical analysis is a fundamental component of pathological diagnosis. KIT (CD117) protein expression is found in about 95% of GIST cases, DOG1 protein expression in 95–98%, and CD34 expression in 70–80% of tumors. Of considerable diagnostic importance is that a positive immunohistochemical reaction for DOG1 is also observed in about half of patients with GIST who do not express the KIT protein [12]. A negative immunohistochemical reaction for SDHB is a characteristic feature of SDH-deficient GISTs and allows their identification in clinical practice [9].

It should be emphasized that modern GIST diagnosis should not rely solely on histological and immunohistochemical findings. The final classification of the tumor and assessment of eligibility for targeted therapy require molecular testing, which is now the diagnostic standard for GIST.

About 80% of GISTs contain activating mutations in the KIT or PDGFRA genes, leading to constitutive ligand-independent activation of tyrosine kinase receptors [13, 14]. This results in sustained activation of key intracellular signaling pathways, particularly the RAS/RAF/MEK/MAPK, PI3K/AKT/mTOR, and JAK/STAT pathways, which are responsible for enhanced proliferation, inhibition of apoptosis, and increased survival of tumor cells [15]. These abnormalities play a key role in initiating and sustaining the oncogenic process in most cases of GIST.

The vast majority of KIT mutations are somatic; they are most commonly located in exon 11, and less frequently in exons 9, 13, and 17 [14]. A distinct subgroup consists of deletions affecting codons 557 and 558 of exon 11, which occur in approximately 28% of patients with GIST and are associated with adverse biological characteristics of the tumor, such as a high mitotic index (> 5/50 HPF) and larger size (> 5 cm) [16]. Tumors with this molecular signature occur in both gastric and extragastric locations, and the diagnosis is most commonly made in patients under the age of 60 years. The frequency of KIT mutations in exon 11, depending on tumor location (stomach vs extragastric sites), varies across studies. Regardless of these differences, KIT mutations in exons 9, 13, and 17 are clearly more frequently observed in small intestinal GISTs. Furthermore, the presence of mutations in exons 9 and 13 is associated with a tendency towards a more aggressive tumor phenotype [7].

PDGFRA-mutant GISTs account for about 10–15% of all cases and are predominantly of the epithelial type, with the stomach being the most common site [15]. The most frequent mutations are those in exon 18 of PDGFRA, and their presence is generally associated with a better prognosis than KIT mutations in exons 9 and 11. An exception is the p.D842V missense mutation, which is characterized by primary resistance to imatinib and other conventional tyrosine kinase inhibitors [16]. Other PDGFRA mutations in exon 18 are considered sensitive to imatinib, whereas rarer mutations in exon 14 are associated with a relatively favorable clinical course.

The molecular profile of GIST is a key predictor of the efficacy of tyrosine kinase inhibitor treatment. Tumors with a KIT mutation in exon 11 are highly sensitive to imatinib, while the presence of KIT mutation in exon 9 correlates with reduced effectiveness of the standard dose of the drug. Despite an initial response to treatment, some patients with GIST develop secondary resistance to imatinib, leading to the progression of one or more neoplastic lesions, usually after 12–36 months of therapy. The mechanism of resistance is most often due to non-randomly distributed single-nucleotide variants affecting codons within the adenosine triphosphate binding pocket of KIT kinase (exons 13 and 14) or the activation loop (exons 17 and 18). One of the most frequently identified secondary resistance mutations is V654A in exon 13 of the KIT gene [17].

Rare Molecular Abnormalities in GISTs and Their Clinical Implications

Although activating mutations in the KIT and PDGFRA genes form the molecular basis of the pathogenesis of most GISTs, the spectrum of molecular abnormalities in GISTs is much more complex. It also includes rare variants of these genes, differing in biological effect and clinical significance, as well as molecular abnormalities in pathways other than those related to KIT and platelet-derived growth factor receptor, which are found in wild-type GISTs. These subgroups are characterized by distinct mechanisms of tumorigenesis and progression, varying sensitivity to targeted therapy, and substantial clinical heterogeneity. The molecular landscape of GIST, including both canonical and rare molecular alterations, is summarized in Fig. 1. A detailed understanding of these abnormalities provides the basis for a more comprehensive molecular classification of GISTs and supports the further development of personalized treatment strategies.

Fig. 1.

Molecular abnormalities leading to the development of gastrointestinal stromal tumors [18–24]. Schematic overview of the principal signaling consequences of activating KIT/PDGFRA mutations (RAS/RAF/MAPK, PI3K/AKT/mTOR, and JAK/STAT pathways) and of alternative drivers in wild-type gastrointestinal stromal tumors, including receptor tyrosine kinases (neurotrophic tyrosine receptor kinase [NTRK], fibroblast growth factor receptor [FGFR], anaplastic lymphoma kinase [ALK]) and succinate dehydrogenase (SDH) deficiency, which through succinate accumulation stabilizes hypoxia-inducible factor 1 alpha (HIF-1α) and impairs TET-mediated demethylation, leading to DNA hypermethylation. Akt (PKB) protein kinase B, ERK extracellular signal-regulated kinase, ETV1 ETS variant transcription factor 1, FOXO3 Forkhead Box O3, GDP guanosine diphosphate, GRB2 growth factor receptor-bound protein 2, GTP guanosine triphosphate, JAK2 Janus kinase 2, MEK mitogen-activated protein kinase kinase, mTORC1 mechanistic target of rapamycin complex 1, PDGFRA platelet-derived growth factor receptor alpha, PI3K phosphatidylinositol 3-kinase, PIP₂ phosphatidylinositol 4,5-bisphosphate, PIP₃ phosphatidylinositol 3,4,5-trisphosphate, RAS rat sarcoma viral oncogene homolog, STAT3 signal transducer and activator of transcription 3, TET enzymes ten-eleven translocation dioxygenases. Created in BioRender. Kisielewska, K. (2026) https://BioRender.com/ppizhjn

Rare Mutations in the KIT Gene

In addition to the typical KIT gene mutations in exon 11 and the slightly less common mutations in exon 9, rare primary KIT mutations in exons 13 and 17 have also been reported [25, 26]. It is estimated that combined they account for approximately 1–2% of all GIST cases [27]. Exon 13, together with exon 14, encodes the adenosine triphosphate-binding pocket in tyrosine kinase domain 1, whereas exon 17, together with exon 18, encodes the activation loop in tyrosine kinase domain 2 [27]. The conformational and functional effects of primary mutations in these regions on KIT receptor activity have not yet been fully elucidated [28]. It should also be emphasized that primary KIT mutations in exons 13 and 17 should not be confused with secondary mutations in the same exons, which are responsible for the development of imatinib resistance in first-line treatment [29].

A clinicopathological analysis conducted in a multicenter study showed that 32 (97%) of the 33 identified mutations in exon 13 of the KIT gene were the 1945A>G substitution, while 15 (71.4%) of the 21 mutations in exon 17 were the 2487T>A substitution [26]. Most of the tumors had spindle-cell morphology. Mutations in exon 13 of the KIT gene were most common in gastric GISTs, whereas mutations in exon 17 were about twice as frequent in small intestinal GISTs compared with gastric GISTs. It has been documented that gastric GISTs with the KIT exon 13 mutation are associated with a higher risk of progression than typical gastric GISTs. In contrast, the risk of progression of small intestinal GISTs with mutations in exon 13 or 17 did not differ significantly from the risk seen in other GISTs in this location.

Data on the efficacy of imatinib in patients with primary KIT mutations in exons 13 and 17 are limited. Mutational analysis of pathological samples from a phase II study on the use of imatinib in GIST revealed that two out of two patients with KIT exon 13 mutations achieved a partial response (PR), while among the two patients with KIT exon 17 mutations, one achieved PR and the other experienced progression of the disease [29]. In the CALGB 150105 study, two of the five patients with KIT exon 13 mutations treated with imatinib achieved PR, one had stabilization of the disease, and one developed progression of the disease. Among the four patients with KIT exon 17 mutations, one achieved PR, two had stabilization of the disease, and one experienced progression of the disease [30].

Mutations in exon 8 of the KIT gene are extremely rare molecular abnormalities in GIST, with an estimated frequency of less than 0.5%. In a registry comprising 145 GISTs initially classified as wild type because of the absence of typical KIT and PDGFRA mutations, two cases of primary GISTs were detected with an identical mutation in KIT exon 8 (c.1255_1257delGAC), resulting in a deletion of aspartic acid at position 419 (p.D419del). One patient was classified as being at high risk of disease progression according to National Comprehensive Cancer Network (NCCN)-Armed Forces Institute of Pathology (AFIP) criteria and developed metastatic disease 29 months after surgery; he did not receive imatinib because the diagnosis had been made before its routine use. The second patient, classified as being at intermediate risk, received adjuvant imatinib and showed no signs of recurrence 24 months after surgery. Both primary tumors were located in the small intestine [30].

A Japanese study identified three cases of GIST with KIT exon 8 mutations among approximately 1000 sporadic GIST cases. In one patient, the p.D419del deletion described above was found in small intestinal GIST, and metastatic disease developed 7 years after the initial surgery [31]. The patient responded to imatinib, which was used as first-line palliative treatment, for 22 months; following disease progression, sunitinib was administered, resulting in disease control for an additional 16 months; the patient died 13 years and 3 months after initial resection. In the other two patients, duodenal GIST was found with a substitution of three amino acids at positions 417–419 (ThrTyrAsp→Tyr). In one of them, metastatic disease developed 2 years after resection of a 3.5-cm tumor, and treatment with imatinib kept the disease under control for 18 months. The other patient, who had a duodenal GIST measuring 8.5 cm in diameter, received adjuvant imatinib and showed no signs of recurrence at the time of publication. All three GISTs with KIT exon 8 mutations in that study were characterized by a high mitotic index [31]. Figure 2 illustrates the distribution of classical and rare KIT/PDGFRA mutations within the receptor structure and highlights their contribution to aberrant signaling pathways involved in GIST development.

Fig. 2.

Role of classical and rare mutations in the KIT/PDGFRA genes in the pathogenesis of gastrointestinal stromal tumors (GISTs) [22, 32–36]. Diagram mapping mutations to the functional domains of the KIT and platelet-derived growth factor receptor alpha (PDGFRA) receptors (extracellular, transmembrane, juxtamembrane, and kinase domains: ATP-binding domain [tyrosine kinase domain 1] and activation loop [tyrosine kinase domain 2]), with their approximate frequencies and reported sensitivity to tyrosine kinase inhibitors (imatinib, sunitinib, regorafenib, ripretinib, avapritinib). Colors indicate sensitivity, intermediate sensitivity or resistance; purple denotes mutations reported in familial GIST, ATP adenosine triphosphate, TKI tyrosine kinase inhibitor, * limited evidence available; sensitivity considered probable. Created in BioRender. Kisielewska, K. (2026) https://BioRender.com/p4w2zg7

Rare Mutations in the PDGFR Gene

Mutations in the PDGFRA gene occur in approximately 15% of GISTs. They are most commonly represented by the p.D842V mutation, which is responsible for about 60% of all PDGFRA mutations and is located in exon 18, which encodes the activation loop of the platelet-derived growth factor alpha receptor. This change is clinically significant because of primary resistance to imatinib [37].

The NAVIGATOR study (phase I) confirmed that avapritinib is highly active against mutations resistant to standard kinase inhibitors (such as imatinib or sunitinib). In patients with the mutation, the objective response rate was 91%, including 13% complete responses.

The median progression-free survival in these patients was 34 months. These results provided the basis for the US Food and Drug Administration and European Medicines Agency approval of avapritinib as first-line treatment for metastatic or unresectable GIST with a mutation in exon 18 of the gene.

This subsection focuses on rare PDGFRA mutations, including less common variants other than p.D842V in exon 18, rare exon 12 mutations affecting the juxtamembrane domain, which account for approximately 1% of all GISTs, and extremely rare mutations in exon 14 encoding the adenosine triphosphate-binding domain, occurring in less than 1% of cases [37]. A retrospective study of patients with GIST treated in European reference centers showed that tumors with PDGFRA mutations in exon 18 other than p.D842V and with mutations in exon 12 were sensitive to imatinib, in contrast to GISTs with the p.D842V mutation, which were resistant to this treatment [38]. The median progression-free survival in this group was comparable to the values observed in patients with a KIT exon 11 mutation. These tumors tended to occur in the stomach, and most of them tested positive for CD117/KIT in immunohistochemical analysis (49 of 58 PDGFRA-mutated GISTs, 85%). No clear conclusions were drawn regarding the efficacy of second-line treatment, as only 11 of the 32 patients receiving second-line therapy were treated with sunitinib. Nevertheless, progression-free survival was numerically longer in patients with PDGFRA mutations other than p.D842V than in those patients with the p.D842V mutation treated in the second-line setting. In addition, a single case report demonstrated an exceptionally good response to sunitinib in a patient with an exon 12 PDGFRA mutation [37].

With regard to the extremely rare PDGFRA mutations in exon 14, a retrospective analysis of 200 GIST tumors in which no mutations were found in exons 9, 11, 13, and 17 of the KIT gene or in exons 12 and 18 of the PDGFRA gene revealed the presence of a mutation at codon 659 (N659) of exon 14 in 11 cases [14]. Eight tumors contained the N659K mutation, while three carried the N659Y mutation. All the neoplasms were located in the stomach, and 10 of the 11 had epithelial morphology. Only 6 of the 11 tumors were CD117/KIT positive on immunohistochemical analysis, although in two cases this expression was limited to small clusters of cells or isolated scattered positive cells. Based on the size of the lesion and the mitotic index, nearly half of these neoplasms were classified as having an aggressive phenotype. However, long-term clinical observation suggested a relatively mild course of the disease, albeit with a limited number of cases analyzed. Although there are no clinical data on the efficacy of treatment with tyrosine kinase inhibitors in this patient group, in vitro studies have reported sensitivity to imatinib in cell models harboring the PDGFRA N659K isoform [14].

Molecular Abnormalities Other Than in the KIT/PDGFRA Genes: Wild-Type GISTs

There is a small but clinically significant subset of GISTs in which no mutations are found in the KIT and PDGFRA genes, collectively referred to as wild-type GISTs. These tumors are characterized by distinct pathogenic mechanisms and specific molecular profiles, which translates into diverse clinical courses and responses to targeted therapy. Understanding the molecular basis in such cases can help assess the risk of an unfavorable disease course and potentially aid in selecting an effective treatment.

Succinate Dehydrogenase (SDH)-Deficient Wild-Type GIST

Succinate dehydrogenase (SDH) is a mitochondrial enzyme complex located in the inner mitochondrial membrane, which participates in both the citric acid cycle and the respiratory chain (complex II) [39]. It catalyzes the oxidation of succinate to fumarate, accompanied by the reduction of FAD to FADH₂. The SDH complex consists of four subunits (SDHA, SDHB, SDHC, SDHD) that cooperate in transferring electrons to ubiquinone [39, 40]. Defects in any component of the SDH complex lead to the destabilization of the entire enzyme, resulting in the degradation of the SDHB subunit. For this reason, the loss of SDHB expression in immunohistochemical analysis is a highly sensitive marker of SDH deficiency, regardless of which subunit of the complex is initially affected [9, 41].

Mutations in SDH genes lead to SDH inactivation and the accumulation of succinate in mitochondria [12]. Elevated levels of succinate, in turn, act as an oncometabolite by stabilizing hypoxia-inducible factor 1α, which promotes the transcription of genes involved in angiogenesis, proliferation and glycolysis. Succinate dehydrogenase-deficient GISTs are defined as tumors that do not express SDHB in immunohistochemical analysis [40]. They are a biologically and clinically distinct subgroup of wild-type GISTs, characterized by a unique molecular profile, clinical course, and different response to systemic therapy.

Most cases of SDH-deficient GIST (about 80%) are associated with germline pathogenic variants in the SDHx genes (SDHA, SDHB, SDHC, SDHD), whereas the remaining approximately 20% of cases result from epigenetic inactivation of the SDHC gene through hypermethylation of the promoter region. Among germline variants, SDHA mutations are the most commonly identified, accounting for up to 50% of GIST cases with SDH deficiency, while mutations in the SDHB, SDHC, and SDHD genes together represent 20–‍30% of cases [40, 41]. Given the potential for pathogenic variants in any SDHx gene, comprehensive germline testing of the entire SDHx panel is recommended for patients with SDH-deficient GISTs [41].

An important clinical issue is the variable and incomplete penetrance of SDHx mutations, which means that many patients have no positive family history of GIST or paraganglioma. The absence of an adverse family history should therefore not be used as an argument against performing genetic testing.

Succinate dehydrogenase-deficient GISTs usually occur in young patients, most often before the age of 40 years, with a marked predominance of cases in women. These tumors are almost always located in the stomach, with a particular tendency to appear in the pyloric region and the lesser curvature [42]. Characteristic morphological features include an epithelioid or mixed (epithelioid-spindle) structure, the frequent presence of multiple tumor foci, lymphatic invasion, and lymph node metastasis. In immunohistochemical analysis, SDH-deficient GISTs typically express KIT/CD117 and DOG1, despite the absence of a KIT mutation [9, 12]. Although these tumors often meet the histological criteria for malignancy, their clinical course is usually indolent compared with other wild-type GISTs. At the same time, SDH-deficient GISTs show some resistance to imatinib.

Surgery remains the mainstay of treatment for SDH-deficient GISTs at the localized stage. In a retrospective analysis from a pediatric clinic and the NIH WT GIST cohort, 71% of patients experienced tumor recurrence or disease progression after surgical treatment. The risk of recurrence or progression was associated with a high mitotic index and the presence of metastases, whereas no correlation was found with microscopic surgical margins. Repeated surgical resections correlate with ever shorter progression-free survival and shorter overall survival, so they should be considered only for palliative purposes, such as in cases of gastrointestinal obstruction or bleeding [43].

Because of resistance to imatinib, this drug should not be used either as adjuvant therapy or in advanced disease [44]. Although the overall efficacy of tyrosine kinase inhibitors remains limited, a relatively better response is observed with sunitinib and regorafenib, most likely owing to their stronger antiangiogenic effects [45, 46]. Promising preliminary results have also been obtained for olverembatinib, a third-generation oral kinase inhibitor, which demonstrated activity in a phase Ib/II study in patients with refractory SDH-deficient GIST—partial responses were seen in some patients, and disease stabilization in the others. Updated results presented at the ASCO 2024 conference showed a clinical benefit rate (complete response + partial response + stabilization of the disease > 4 cycles) of 92.3%, which warrants further research.

A key finding is the preferential hypermethylation of the MGMT gene promoter in SDH-deficient GISTs compared with tumors with normal SDH activity, which in combination with metabolic abnormalities supports the concept of sensitivity to temozolomide [40]. In the study by Yebra et al., temozolomide achieved a 100% disease control rate and an objective response rate of 40%, with a median overall survival of 1.9 years, providing a strong rationale for further clinical studies [47]. An interesting therapeutic approach involves combining temozolomide with a DR5 receptor agonist (INBRX-109), which in in vitro models enhanced the cytotoxic effect by increasing endoplasmic reticulum stress and upregulating DR5 expression; a phase I clinical trial is currently underway. Other strategies under investigation include the use of an insulin-like growth factor-1 receptor inhibitor (linsitinib), which in a phase II study enabled 40% of patients to achieve disease control for more than 9 months, and epigenetic drugs such as guadecitabine, but with no significant objective responses [48, 49]. Guadecitabine, a DNA methyltransferase inhibitor that induces global demethylation, has been evaluated in patients with SDH-deficient tumors, including GIST; however, no objective responses to treatment were noted, with only prolonged disease stabilization observed in some patients (four out of nine) (Fig. 3).

Fig. 3.

Molecular consequences of succinate dehydrogenase (SDH) deficiency in cells and the pathogenesis of gastrointestinal stromal tumors [50]. Loss of function of the SDH complex (SDHA/B/C/D) disrupts the tricarboxylic acid (TCA) cycle and respiratory chain, causing succinate accumulation. Succinate inhibits α-ketoglutarate–dependent dioxygenases, including prolyl hydroxylases (stabilizing hypoxia-inducible factor 1 alpha [HIF-1α]), TET methylcytosine dioxygenases, and JmjC-domain histone demethylases, resulting in impaired DNA demethylation, global DNA hypermethylation, altered histone methylation, and metabolic reprogramming toward a glycolytic phenotype. JmjC Jumonji C-domain-containing histone demethylases, TET ten-eleven translocation dioxygenases, VEGF vascular endothelial growth factor. Created in BioRender. Kisielewska, K. (2026) https://BioRender.com/d42g3jb

Triple-Negative GIST

Gastrointestinal stromal tumors that do not have mutations in the KIT and PDGFRA genes and do not lack SDH (SDH-competent wild-type GISTs) may be referred to as “triple-negative” GISTs. The most commonly reported molecular alterations in this group are aberrations in the RAS/RAF/MAPK pathway, mainly resulting from a BRAF V600E mutation or loss-of-function mutations in the NF1 gene [41, 51–54].

BRAF V600E-mutated GISTs are a rare subtype, accounting for approximately 1–3% of all GISTs, whereas among wild-type GISTs, the frequency of BRAF mutations varies widely, from 3.9% to 20%. In general, BRAF mutations appear to be mutually exclusive with KIT and PDGFRA mutations, hence BRAF V600E mutations are not usually expected to occur in KIT- or PDGFRA-mutated GISTs. However, reports of the simultaneous detection of the KIT exon 11 mutation and the BRAF V600E mutation in a series of 53 patients challenged this concept and led to the hypothesis that BRAF mutation may be a potential mechanism of resistance [55, 56]. In another study, the BRAF V600E mutation was detected in 8 of 35 GISTs with the KIT/PDGFRA mutation using droplet digital polymerase chain reaction. These results, however, have not been confirmed by alternative methods, such as allele-specific polymerase chain reaction or dideoxy sequencing, suggesting that the detected changes may have been limited to only small tumor subclones, and their biological role should be interpreted with caution. In contrast, in a large series of 407 GIST cases, no BRAF mutation was detected in any KIT- or PDGFRA-mutated tumor, while a single case of BRAF mutation was identified in a wild-type KIT/PDGFRA GIST.

BRAF V600E-mutated GISTs occur with similar frequency in both sexes and do not differ significantly from other GISTs in terms of morphology and immunophenotype [28]. Because of its high sensitivity and specificity, VE1 immunohistochemical staining is recommended as a screening tool for detecting the presence of a BRAF mutation, although caution is required when interpreting weak staining, which can occur in both BRAF-positive and BRAF-negative tumors [57]. While BRAF-mutated GIST has been reported in various anatomical locations, including the esophagus, stomach, duodenum, small intestine, rectum, and peritoneum, the majority of cases involved the small intestine. In an analysis of 37 cases of BRAF-mutated GIST, as many as 25 tumors were located in the small intestine. Tumors classified as high risk according to the Miettinen and Lasota criteria were observed more frequently—the detailed analysis indicated no risk of recurrence in 4 cases, very low risk in 3, low risk in 7, intermediate risk in 5, and high risk in 12 cases [58]. Ultimately, the exact prognostic value of the BRAF V600E mutation is unclear and requires further research.

Surgery remains the mainstay of treatment for BRAF-mutated GISTs at the localized stage [59]. In advanced disease, it is recommended to consider therapies targeting BRAF kinase inhibition, based on reports of objective responses to dabrafenib and the Food and Drug Administration’s accelerated approval of the combination of dabrafenib and trametinib for the treatment of BRAF-mutated GIST. The NCCN guidelines also include the possibility of neoadjuvant treatment with BRAF/MEK inhibitors in situations where a reduction in tumor size may limit the extent of surgery.

KRAS mutations are extremely rare molecular abnormalities in wild-type GIST and are found in less than 1% of all cases. In a series of 514 GISTs, comprising 117 wild-type tumors, not a single case of KRAS mutation was detected using either Sanger sequencing or pyrosequencing [60]. Nevertheless, the literature contains reports of individual clinical cases of patients diagnosed with KRAS-mutated wild-type GIST. One patient was reported to have a small intestinal GIST with an intermediate risk of recurrence and the G12D mutation; the second case involved a patient with a small intestinal GIST carrying the G13D mutation and a high risk of recurrence [61]. These tumors did not differ in their morphological and immunohistochemical characteristics from classical KIT/PDGFRA-mutated GISTs. In a retrospective analysis of 38 patients with GISTs, the KRAS G12D mutation was identified in one patient with an aggressive gastric wild-type GIST who experienced rapid recurrence after surgery and had a short overall survival despite treatment with imatinib [62]. In another publication, 267 GISTs were retrospectively evaluated, and one case of a gastric wild-type GIST with KRAS G12V mutation was identified, where the tumor had anaplastic features, lacked SDHB expression, and was resistant to various tyrosine kinase inhibitors [63]. In yet another analysis, the KRAS G13D mutation was detected in one of 146 wild-type GISTs examined; however, the paper did not include data on the location or clinical course [64].

Imatinib is not expected to be effective in patients with KRAS-mutated GIST, and therefore its use in this patient group is not recommended either as adjuvant therapy or in advanced disease. KRAS G12D inhibitors and other strategies targeting this pathway, currently in early clinical trials, offer therapeutic hope.

An alternative to KRAS mutation being the only molecular abnormality in GIST is that KRAS mutations coexist with KIT or PDGFRA mutations. In a retrospective analysis of 60 patients diagnosed with GIST, cases were identified of concurrent KRAS G12D or G13D mutations with KIT exon 11 deletions, as well as of KRAS G13D coexisting with PDGFRA D842V (none of these patients had previously received imatinib) [65]. In an additional analysis performed on cell lines, the authors demonstrated that although imatinib blocks the constitutively active KIT receptor, it does not inhibit the activation of the ERK pathway, which also depends on mutant KRAS in cells co-transfected with KIT and KRAS genes, nor does it induce the phenotypic effects observed in cells lacking KRAS mutation. Ultimately, the findings support recognition of KRAS mutations as one of the mechanisms underlying primary resistance to imatinib. In a published case report, a patient with gastric GIST harboring a KIT exon 11 mutation developed bifocal disease progression after an initial response to imatinib; following surgical resection of both lesions, a KRAS G12R mutation was detected in one of them [65]. It appears that the coexistence of KRAS mutations with KIT or PDGFRA mutations should be considered a potential mechanism of tumor evolution and the development of treatment resistance.

Quadruple-Negative GIST

The absence of mutations in the KIT/PDGFRA genes, along with SDH deficiency and abnormalities in the RAS/RAF/MAPK pathway, result in GIST being classified as “quadruple-negative”. In this heterogeneous group of GISTs, several alternative molecular mechanisms have been identified that may act as drivers of tumorigenesis. One of these is the fibroblast growth factor receptor 1 (FGFR1) pathway. The literature describes both gain-of-function mutations in the FGFR1 receptor itself and fusions involving this gene. There have also been reports of FGF4 amplification in wild-type GISTs [10]. Moreover, the FGF3, FGF4, and FGF19 genes, located next to each other on chromosome 11q13, are frequently co-amplified and encode ligands for the FGFR1 receptor.

Interestingly, it has been shown as well that SDH-deficient GISTs are characterized by increased FGF4 expression due to dysfunction of the insulator separating the super-enhancer from the FGF4 gene, caused by DNA hypermethylation [42]. The role of the FGFR pathway in the pathogenesis of GIST is also confirmed by clinical observations indicating the efficacy of regorafenib — a tyrosine kinase inhibitor with activity against FGFR — in both wild-type GIST and SDH-deficient GIST. This suggests that FGFR signaling may be an important therapeutic target in this group of tumors.

A review of the available literature identified several less common potential drivers of quadruple-negative GISTs. To date, NTRK3 fusions, among others, have been described; these can be effectively treated with NTRK-targeted tyrosine kinase inhibitors such as larotrectinib or entrectinib [66, 67]. Individual reports have also identified mutations in the E3 ubiquitin ligase CBL, KIT-PDGFRA fusion, and ARID1A as potential pathogenic mechanisms [68]. Whole-exome sequencing performed on a small series of nine quadruple-negative GISTs revealed oncogenic somatic mutations in the TP53, MEN1, MAX, FGFR1, CHD4, and CTDNN2 genes [69].

Another paper described two cases of quadruple-negative GIST with a different gene expression profile from other GISTs; these were marked by overexpression of CALCRL, COL22A1, NTRK2, CDK6, ERG, and other genes [70]. A study of 72 quadruple-negative GISTs in the Chinese population found TP53 and RB1 mutations in 27.78% and 25% of patients, respectively. Mutations have also been identified in many other genes, such as ALK, CCNE1, MYC, PIK3CA, POLE, and PTEN, although their role as driver mutations remains unclear [52]. Alterations in other pathways are even rarer, but one is the DNA damage response pathway in the presence of CHEK2 and FANCA mutations [71, 72] (Table 1).

Table 1.

Summary of rare mutations identified in wild-type GISTs, including data on the clinical course and treatment sensitivity

Wild-type GIST subtype	Primary molecular abnormality	Clinicopathological features	Potential therapies/clinical notes	References
SDH-deficient GISTs	Germinal mutations in SDHA/B/C/D or epimutation of the SDHC promoter; loss of SDHB expression	Age under 40 years, predominantly women, stomach, multiple tumors, lymph node metastases; often clinically indolent	Surgery; low sensitivity to imatinib; relatively good response to sunitinib/regorafenib; experimental therapies	[12, 44]
Carney triad	SDHC epimutation (promoter hypermethylation); previously proposed 1q deletion (SDHC)	Non-hereditary; almost exclusively women; SDH-deficient GISTs, pulmonary chondromas, paragangliomas; synchronous or metachronous components	Consider genetic testing; there may be phenotypic overlap with other syndromes	[73]
BRAF V600E-mutated GISTs	Activating BRAF mutation	Mainly the small intestine; spindle-shaped morphology; variable clinical course	Surgery; BRAF ± MEK inhibitors (e.g., dabrafenib + trametinib)	[74]
NF1-associated GISTs	NF1 LoF mutations → activation of the RAS/RAF/MAPK pathway	Heterogeneous group; often small intestine	No response to imatinib; surgical treatment; studies on MEK inhibitors	[75]
FGFR-activated GISTs	FGFR1 GOF mutations, FGFR1 fusions, FGF3/4/19 amplifications	Heterogeneous presentation; sometimes triple or quadruple WT GIST	Regorafenib (depending on the FGFR pathway); potential FGFR inhibitors	[66, 70]
GISTs with NTRK fusions	NTRK1/2/3 fusions (e.g., ETV6-NTRK3)	Rare; no characteristic phenotype	NTRK inhibitors (larotrectinib, entrectinib)	[66, 67]
KRAS-mutated GISTs	KRAS mutations (e.g., G12D, G13D)	Often aggressive course, resistance to TKIs	Lack of efficacy of imatinib; studies on KRAS inhibitors	[74]
GISTs with DNA damage response defects	Mutations in CHEK2, FANCA, and other DNA repair genes	Limited data	Potential PARP inhibitors (hypothesis)	[76]
Quadruple-negative GISTs	No KIT/PDGFRA mutations, no SDH deficiency, no RAS/RAF/MAPK alterations	Heterogeneous group with diverse features	NGS diagnostics crucial to identify mutations; targeted therapies based on the detected condition	[69, 72]

DDR DNA damage repair, FGFR fibroblast growth factor receptor, GIST gastrointestinal stromal tumors, GOF gain-of-function, LoF loss-of function, NGS next-generation sequencing, NTRK neurotrophic tyrosine receptor kinase, SDH succinate dehydrogenase, TKIs tyrosine kinase inhibitors

Hereditary GISTs and Genetic Syndromes

Hereditary and Syndromic SDH-Deficient GISTs

Pathogenic germline variants in SDHx genes are a component of the hereditary paraganglioma-pheochromocytoma syndrome (HPPS), which is associated with an increased risk of developing various neoplasms, including paraganglioma, pheochromocytoma, GIST, and renal cell carcinoma. Genes associated with an increased risk of developing extra-adrenal paragangliomas and adrenal pheochromocytomas also include other predisposing genes, such as SDHAF2, MAX, FH, VHL, RET, DNMT3A, SLC25A11, MDH2, and TMEM127. In patients with HPPS who develop GISTs, these tumors tend to occur at a younger age, often take a multifocal form, may involve lymph nodes, and have a greater tendency to metastasize [77].

Syndromes related to SDH-deficient GISTs include Carney triad and Carney–Stratakis syndrome [73, 78, 79]. Carney triad is a non-hereditary syndrome characterized by the coexistence of SDH-deficient GISTs, pulmonary chondromas, and extra-adrenal paragangliomas, and almost exclusively affects women [79]. These lesions may be synchronous or metachronous and comprise either two or three components of the triad. Initially, it was proposed that the molecular cause of Carney triad was a somatic genomic deletion on chromosome 1q involving the SDHC gene locus; however, subsequent studies confirmed the role of SDHC gene epimutation, due to hypermethylation of the promoter region, in the development of this syndrome [10]. SDHC epimutations are more commonly observed in SDH-deficient GISTs than in paragangliomas and/or pheochromocytomas and occur almost solely in women [68]. In cohort analyses, SDHC epimutations were found in about 20% of SDH-deficient GISTs, although this frequency may be underestimated because of the limited availability of promoter methylation testing [41, 79].

Carney–Stratakis syndrome, in turn, is inherited in an autosomal dominant manner and results from the presence of pathogenic germline variants or large deletions in the SDHB, SDHC, or SDHD genes [80]. Clinically, this syndrome is characterized by the coexistence of multiple extra-adrenal paragangliomas and multifocal gastric GISTs. Unlike Carney triad, Carney–Stratakis syndrome affects both sexes and usually manifests during childhood or adolescence [80]. An important clinical consideration is the possibility that SDHC epimutations may coexist with germline pathogenic variants in the SDHx genes, which is why genetic testing should also be considered in patients with the Carney triad phenotype. Moreover, some patients with germline pathogenic variants in SDHx may present with the clinical phenotype of Carney triad, which further complicates the differential diagnosis of these syndromes [80]. The identification of germline pathogenic variants in the SDHx genes is of great clinical importance, as it influences not only treatment decisions but also the feasibility of cascade testing among family members, thereby enabling the identification of individuals at increased risk of developing HPPS-associated tumors.

Hereditary KIT/PDGFRA Mutations: Germline KIT/PDGFRA Pathogenic Variants

Only a small percentage of GISTs are related to hereditary factors. The possibility of a germline basis for KIT- or PDGFRA-mutated GISTs may be suggested by features such as multiple tumors in a single patient or within a family, as well as a young age at diagnosis. In addition, the presence of identical somatic mutations in multiple primary tumor sites should raise suspicion of a hereditary predisposition. Apart from the HPPS, the hereditary form of GIST is predisposed by the presence of germline KIT/PDGFRA pathogenic variants.

Germline KIT Pathogenic Variants

In families with germline KIT pathogenic variants who have GISTs, concomitant skin hyperpigmentation has been reported [80]. These variants have so far been identified only in a small number of families with GIST, as well as in some families with mastocytosis [64]. Although a genotype–phenotype relationship has been suggested, it cannot be definitively confirmed because of the rarity of these cases [81].

Germline PDGFRA Pathogenic Variants

Germline PDGFRA pathogenic variants are extremely rare. The descriptions of five families highlighted a specific phenotype, including thickened facial skin, broad hands and feet, and premature tooth loss. Multiple GISTs were found in affected individuals, with incomplete penetration of this syndrome observed [82, 83].

GIST in the Context of Neurofibromatosis (Germline Neurofibromatosis Type 1 [NF1] Pathogenic Variants)

Neurofibromatosis type 1 (NF1) is a genetic disorder inherited in an autosomal dominant manner [74, 75, 83]. Its incidence is approximately 1 in 4000–5000. About 50% of cases occur sporadically without a positive family history, which is due to the high frequency of de novo mutations in the NF1 gene. Patients with NF1 are at increased risk of malignant tumors, including malignant tumors of the peripheral nerve sheath, leukemias, and GISTs [78].

The clinical presentation of NF1 includes café-au-lait spots, cutaneous neurofibromas, Lisch nodules, choroidal abnormalities, freckles in flexural areas, and learning difficulties. The disease has nearly 100% penetration rate. Gastrointestinal stromal tumors develop in approximately 7% of patients with NF1 and are most commonly found in the small intestine [84, 85]. Neurofibromatosis type 1-associated GISTs account for approximately 1–2% of all GIST cases.

Neurofibromatosis type 1 results from inactivation of the NF1 tumor suppressor gene, which encodes neurofibromin, a protein acting as a negative regulator of the RAS pathway. Based on case series analyses, it has been demonstrated that NF1-associated GISTs are characterized by a distinct molecular and clinical phenotype. Mutations in the KIT, PDGFRA, BRAF, or SDH genes are not typically found in them. These tumors are more common in younger patients, tend to be multifocal, have low mitotic activity as well as a predominant spindle cell morphology and location in the small intestine, and their clinical course is usually indolent [65, 86, 87].

Surgery remains the mainstay of treatment for localized disease. In the metastatic stage, the prognosis is poor, and participation in clinical trials should be considered if available [88, 89]. The tumors are resistant to imatinib and other tyrosine kinase inhibitors because their pathogenesis is based on constitutive activation of the RAS pathway rather than on the activation of receptor tyrosine kinases [89]. However, a single case of a partial metabolic response to regorafenib has been seen on positron emission tomography-computed tomography scan [90]. Because systemic treatment options are limited, a strategy of close monitoring may be considered for slow-growing tumors, while in symptomatic disease, the use of palliative local-regional treatment is acceptable.

Targeting the MAPK/MEK pathway is a rational therapeutic approach in NF1. A MEK inhibitor, selumetinib, has been shown to induce durable tumor regression and produce clinical benefit in children with NF1 and inoperable plexiform neurofibromas. To date, no clinical studies have been conducted to evaluate RAS/MEK pathway inhibitors in NF1-associated GISTs. A National Cancer Institute-sponsored trial (NCT03109301) evaluating selumetinib in patients with NF1-mutated GISTs was terminated early because of slow patient recruitment (Table 2).

Table 2.

Summary of data on the clinical and molecular characteristics of hereditary GISTs

Subtype/syndrome	Primary molecular abnormality	Clinicopathological features	Potential therapies/clinical notes	References
SDHx (HPPS)	Germline pathogenic variants in the SDHx genes, SDHA/B/C/D germline mutations	Early age at diagnosis; often multifocal; possible lymph node involvement; increased tendency to metastasize; coexistence of paraganglioma/pheochromocytoma and other neoplasms (including RCC)	Importance of genetic testing; possibility of cascade testing in the family	[40, 46]
Carney–Stratakis syndrome	Germline pathogenic variants or deletions in SDHB/SDHC/SDHD	Autosomal dominant inheritance; both sexes; onset in childhood/ adolescence; multiple paragangliomas and multifocal gastric GISTs	Genetic testing; differentiation from Carney triad; possible SDHC epimutations	[91, 92]
Germline KIT PV	Germline KIT pathogenic variants	Rare; multiple GISTs; possible skin hyperpigmentation; also reported in families with mastocytosis	No clear genotype–‍phenotype correlation; limited data	[93, 94]
Germline PDGFRA PV	Germline PDGFRA pathogenic variants	Very rare; multiple GISTs; incomplete penetration; phenotype: thickening of the facial skin, broad hands/feet, premature tooth loss	Limited data; characteristic clinical phenotype	[82, 83]
GIST in the context of NF1	Inactivation of the NF1 gene → activation of the RAS pathway	Incidence of NF1: ~ 1:4000–5000; ~ 50% de novo mutations; GIST in about 7% of patients; usually the small intestine; multifocality; low mitotic activity; spindle cell morphology; indolent course; no KIT/PDGFRA/BRAF/SDH mutations	Surgery for localized disease; resistance to imatinib and other TKIs; possible palliative treatment; observation for slow-growing tumors; potential approaches: MEK inhibitors (e.g., selumetinib – no studies in NF1 GISTs); participation in clinical trials to be considered	[90]

GIST gastrointestinal stromal tumors, HPPS hereditary paraganglioma-pheochromocytoma syndrome, PDGFRA platelet-derived growth factor receptor alpha, PV pathogenic variant, RCC renal cell carcinoma, SDH succinate dehydrogenase, TKIs tyrosine kinase inhibitors

Recommendations for Molecular Testing in Patients with GIST

Molecular testing is currently a key component of GIST diagnostics and is recommended by all major expert groups as a tool for confirming the diagnosis, predicting response to systemic therapy, and optimizing treatment selection. The European Society for Medical Oncology guidelines emphasize that mutation analysis should be part of the routine diagnostic procedure for most patients. According to the European Society for Medical Oncology, molecular testing may be omitted only for small (< 2 cm) tumors located outside the rectum, which in clinical practice rarely require systemic therapy [95]. From a practical point of view, as indicated by the NCCN as well as Canadian and British guidelines, molecular testing is particularly important in patients scheduled to undergo systemic therapy for any purpose—palliative, neoadjuvant, or adjuvant in GISTs with a high risk of recurrence—and should be performed in this patient group.

The highest level of evidence and recommendations (IA) for molecular testing in patients with GIST include testing for KIT and PDGFRA mutations and immunohistochemical evaluation of SDHB in the absence of mutations in these genes. At the same time, all the guidelines reviewed highlight the need for in-depth molecular testing in cases with no detectable mutations in these genes; as the European Society for Medical Oncology notes, molecular testing may have to be performed at a reference center. The NCCN guidelines recommend that all wild-type GISTs be tested for SDH deficiency and other driver mutations using next-generation sequencing techniques. The British Sarcoma Group proposes a sequential diagnostic algorithm that includes assessment of SDHB expression (via immunohistochemistry), followed by analysis of NF1 mutations, and subsequently testing for BRAF/RAS mutations and NTRK rearrangements [96]. Similarly, Polish guidelines advocate the use of next-generation sequencing methods in such situations [97].

Identifying SDH-deficient GISTs, which account for the majority of wild-type GIST cases, is an important step in the diagnostic process. Both the British Sarcoma Group and Canadian experts recommend performing SDHB immunohistochemistry as a screening test, especially when clinicopathological features are atypical (e.g., young age, gastric location, multifocality, lymph node metastases). In cases of loss of SDHB expression, further genetic testing is recommended, including assessment of SDHx gene mutations and potential epigenetic abnormalities. The Sarcoma European Latin-American Network (SELNET) guidelines on GIST recommend testing for KIT and PDGFRA mutations in candidates for systemic therapy, but do not provide detailed information regarding SDH immunohistochemistry. According to Japanese clinical practice guidelines for GIST, an initial SDHB immunohistochemical analysis is recommended for all epithelioid GISTs or those with suspected SDH abnormalities. Analysis of somatic mutations in this gene is recommended for KIT-negative or KIT-weakly-positive GIST and for GIST initially resistant to imatinib [98]. Ideally, a SDH immunohistochemical evaluation should be performed routinely in patients diagnosed with wild-type GISTs to guide further treatment if imatinib proves ineffective.

Another important aspect is the identification of patients requiring germline testing. The NCCN and British Sarcoma Group guidelines indicate that testing for hereditary GISTs should be considered in patients with clinical suspicion of hereditary syndromes, including cases of multiple tumors, young age at diagnosis, the presence of an NF1-associated or SDH-deficient GIST, and a positive family history [96]. The specific indications for genetic testing for hereditary SDH-deficient GISTs are detailed in the recommendations of the French expert group and are as follows: loss of SDHB expression, a family history of GIST, a diagnosis of multiple GISTs, diagnosis before the age of 30 years, or association with paraganglioma [68] (Fig. 4).

Fig. 4.

Molecular diagnostic algorithm for patients with gastrointestinal stromal tumors (GISTs), taking clinical characteristics into account. Stepwise diagnostic algorithm integrating histopathological confirmation (CD117/DOG1), KIT/PDGFRA testing, SDHB immunohistochemistry for wild-type tumors, and extended molecular testing (RAS, BRAF, PI3K, NTRK, TP53, FGFR fusions, ALK) for SDH-competent wild-type GIST, together with indications for genetic counseling and germline testing and the recognition of familial/syndromic GIST (neurofibromin 1 [NF1] associated, succinate dehydrogenase [SDH] deficient, Carney–Stratakis syndrome, Carney triad). IHC immunohistochemistry, SDHx SDH subunit genes. Created in BioRender. Kisielewska, K. (2026) https://BioRender.com/rsz2esq

Summary

Gastrointestinal stromal tumors, though relatively rare, remain the most common sarcomas of the gastrointestinal tract. These tumors are a molecularly heterogeneous group of neoplasms in which the tumor genetic profile largely determines the clinical course of the disease, prognosis, and sensitivity to targeted therapy. Most GISTs are characterized by activating mutations in the KIT proto-oncogene, which encodes the KIT (CD117) receptor tyrosine kinase, and the result of these abnormalities is constitutive activation of the receptor, independent of ligand presence, leading to sustained stimulation of proliferative pathways, inhibition of apoptosis, and uncontrolled proliferation of tumor cells. Although most GISTs are associated with the presence of classical activating mutations in the KIT or PDGFRA genes, a growing body of evidence confirms that a substantial group of patients has less common molecular abnormalities, including both atypical KIT/PDGFRA mutation variants and alterations independent of these genes, typical of wild-type GISTs. These subtypes differ in their pathogenic mechanisms, clinicopathological characteristics, and profiles of sensitivity to tyrosine kinase inhibitors; in many of these tumors, the efficacy of standard systemic therapy is limited.

Gastrointestinal stromal tumors with SDH deficiency, associated with NF1, with BRAF mutations and other rare alterations in the RAS/RAF/MAPK, NTRK, or FGFR pathways are of particular clinical interest, as they may serve as a basis for the use of alternative targeted therapies or for inclusion in clinical trials. Increasing data also suggest that rare molecular alterations may play a role not only as primary drivers of tumors but also as mechanisms of primary or secondary resistance to treatment. In clinical practice, this means that there is a growing need for more in-depth and systematic molecular diagnostics, particularly in patients with atypical clinical presentation, the absence of KIT/PDGFRA mutations, suspected hereditary syndromes, or unexpected treatment failure.

The data presented confirm that the current management of patients with GISTs should be based not only on histological and immunohistochemical diagnosis, but also on precise molecular characterization of the tumor. This approach enables a more accurate biological classification of the neoplasm, better risk assessment, more informed treatment selection, and the identification of patients who may benefit from non-standard therapy or genetic counseling. Based on current knowledge, comprehensive molecular diagnostics should be considered an integral part of modern personalized GIST treatment, and further research into rare molecular variants remains a key area for progress in this field.

Funding

No external funding was received for the preparation of this article.

Declarations

Conflict of Interest

Anna Klimczak has received honoraria for lectures and advisory boards from Bristol-Myers Squibb, Philogen, Amgen, Cogent, and Genesis Pharma. Katarzyna Kisielewska has received honoraria for lectures, manuscript writing, and educational events from BMS, MSD, Pierre Fabre, and Medison Pharma and travel grants from MSD, Genesis Pharma, and Pierre Fabre. Anna Szumera-Ciećkiewicz has no conflicts of interest that are directly relevant to the content of this article. Piotr Rutkowski has received honoraria for lectures and advisory boards from Bristol-Myers Squibb, MSD, Novartis, Pierre Fabre, Philogen, Immunome, Cogent, Genesis Pharma, and Medison Pharma and is a member of IDMC for Erasca.

Ethical Approval

This article is based exclusively on previously published studies and does not contain any new studies involving human participants or animals performed by any of the authors. Therefore, ethics approval was not required.

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Availability of Data and Material

No datasets were generated or analyzed during the current study.

Code Availability

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Author Contributions

AK: conceptualization, literature review, writing (original draft). KK: writing (review and editing), preparation of figures and tables. AS-C: conceptualization, review, supervision. PR: conceptualization, review, supervision.